From 358f0cd5e8f3e23ca059c3fd5c1c5739faaeb425 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 3 Oct 2016 08:06:25 +0000
Subject: Handle JSON override files in startup script

---
 bin/genenetwork2 | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index d926d6a1..872e9326 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,14 +1,19 @@
 #! /bin/bash
 #
-# This will run the GN2 server (with default settings if none supplied). Pass in
-# your own settings file, e.g.
+# This will run the GN2 server (with default settings if none
+# supplied). Pass in your own settings file, e.g.
 #
 #   ./bin/genenetwork2 ~/my_settings.py
 #
+# But better is to retain the defaults and override them with
+# JSON file (see the deploy docs).
+#
+#   ./bin/genenetwork2 ~/my_overrides.json
+#
 # To run a maintenance script with settings (instead of the webserver) add that with
 # a -c switch, e.g.
 #
-#   ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
+#   ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
 #
 # Environment settings can be used to preconfigure as well as a
 # settings.py file.
@@ -23,10 +28,11 @@ if [ -d $GN2_GUIX_PATH ]; then
 fi
 echo $GN2_BASE_PATH
 
-# Handle settings parameter
+# Handle settings parameter (can be .py or .json)
 settings=$1
-if [ -z $settings ]; then
-    # get default
+ext="${settings##*.}"
+if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
+    overrides=$settings
     settings=$GN2_BASE_PATH/etc/default_settings.py
 else
     shift
@@ -35,7 +41,11 @@ if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
 fi
-export WQFLASK_SETTINGS=$settings
+export WQFLASK_SETTINGS=$settings     # Python
+export WQFLASK_OVERRIDES=$overrides   # JSON
+
+echo WQFLASK_SETTINGS=$settings
+echo WQFLASK_OVERRIDES=$overrides
 
 # We may change this one:
 export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH
-- 
cgit v1.2.3


From 598fbead85b0ecb9127989a9c5a88a2d7bc91a5d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 3 Oct 2016 09:23:57 +0000
Subject: Config: supporting JSON OVERRIDES

---
 bin/genenetwork2            |  2 +-
 wqflask/utility/tools.py    | 35 +++++++++++++++++++++++++++++------
 wqflask/wqflask/__init__.py |  2 +-
 3 files changed, 31 insertions(+), 8 deletions(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 872e9326..30a4dc95 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -56,7 +56,7 @@ if [ -z $TEMPDIR ]; then
 fi
 
 # Now handle command parameter -c
-if [ $1 = '-c' ] ; then
+if [ "$1" = '-c' ] ; then
     cd $GN2_BASE_PATH/wqflask
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 545c0427..23d6fb62 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -3,6 +3,7 @@
 
 import os
 import sys
+import json
 
 from wqflask import app
 
@@ -10,6 +11,8 @@ from wqflask import app
 import logging
 logger = logging.getLogger(__name__ )
 
+OVERRIDES = {}
+
 def get_setting(command_id,guess=None):
     """Resolve a setting from the environment or the global settings in
     app.config, with valid_path is a function checking whether the
@@ -45,13 +48,15 @@ def get_setting(command_id,guess=None):
     logger.debug("Looking for "+command_id+"\n")
     command = value(os.environ.get(command_id))
     if command is None or command == "":
-        # ---- Check whether setting exists in app
-        command = value(app.config.get(command_id))
+        command = OVERRIDES.get(command_id)
         if command is None:
-            command = value(guess)
-            if command is None or command == "":
-                # print command
-                raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
+            # ---- Check whether setting exists in app
+            command = value(app.config.get(command_id))
+            if command is None:
+                command = value(guess)
+                if command is None or command == "":
+                    # print command
+                    raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
     logger.debug("Set "+command_id+"="+str(command))
     return command
 
@@ -169,6 +174,7 @@ def show_settings():
     log_level = getattr(logging, LOG_LEVEL.upper())
     logging.basicConfig(level=log_level)
 
+    logger.info(OVERRIDES)
     logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
     print "runserver.py: ****** Webserver configuration ******"
     keylist = app.config.keys()
@@ -179,7 +185,9 @@ def show_settings():
         except:
             print("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC))
 
+
 # Cached values
+HOME               = get_setting('HOME')
 WEBSERVER_MODE     = get_setting('WEBSERVER_MODE')
 GN_SERVER_URL      = get_setting('GN_SERVER_URL')
 SQL_URI            = get_setting('SQL_URI')
@@ -198,3 +206,18 @@ PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
 PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir()
+
+from six import string_types
+
+if os.environ.get('WQFLASK_OVERRIDES'):
+    jsonfn = get_setting('WQFLASK_OVERRIDES')
+    logger.error("WQFLASK_OVERRIDES: %s" % jsonfn)
+    with open(jsonfn) as data_file:
+        overrides = json.load(data_file)
+        for k in overrides:
+            cmd = overrides[k]
+            if isinstance(cmd, string_types):
+                OVERRIDES[k] = eval(cmd)
+            else:
+                OVERRIDES[k] = cmd
+            logger.debug(OVERRIDES)
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 602246d9..2188ce17 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -8,7 +8,7 @@ from utility import formatting
 
 import logging
 logger = logging.getLogger(__name__ )
-logging.basicConfig(level=logging.WARN)
+logging.basicConfig(level=logging.INFO)
 
 app = Flask(__name__)
 
-- 
cgit v1.2.3


From 3df145309159efd18dadc537ac7eebafef5b4595 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 3 Oct 2016 10:40:21 +0000
Subject: Use of GN2_PROFILE

---
 bin/genenetwork2 | 56 +++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 43 insertions(+), 13 deletions(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 30a4dc95..889401fd 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -17,29 +17,33 @@
 #
 # Environment settings can be used to preconfigure as well as a
 # settings.py file.
+#
+# GN2_BASE_PATH is base directory of wqflask source code
+#
 
 SCRIPT=$(readlink -f "$0")
-GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT"))
+GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
+
+echo GN2_BASE_DIR=$GN2_BASE_DIR
 
-GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg
-if [ -d $GN2_GUIX_PATH ]; then
-  echo GN2 is running from GUIX
-  GN2_BASE_PATH=$GN2_GUIX_PATH
-fi
-echo $GN2_BASE_PATH
 
 # Handle settings parameter (can be .py or .json)
 settings=$1
 ext="${settings##*.}"
 if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
     overrides=$settings
-    settings=$GN2_BASE_PATH/etc/default_settings.py
+    settings=$GN2_BASE_DIR/etc/default_settings.py
 else
     shift
 fi
 if [ ! -e $settings ]; then
-    echo "ERROR: can not locate settings file - pass it in the command line"
-    exit 1
+    GUIX_ETC=$GN2_BASE_DIR/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg
+    if [ -d $GUIX_ETC ]; then
+        echo INFO: GN2 is actually running from GNU Guix
+    else
+        echo "ERROR: can not locate settings file - pass it in the command line"
+        exit 1
+    fi
 fi
 export WQFLASK_SETTINGS=$settings     # Python
 export WQFLASK_OVERRIDES=$overrides   # JSON
@@ -47,17 +51,43 @@ export WQFLASK_OVERRIDES=$overrides   # JSON
 echo WQFLASK_SETTINGS=$settings
 echo WQFLASK_OVERRIDES=$overrides
 
+# ---- Checks and balances
+if [ -z $GUIX_ETC ]; then
+    if [ -z $GN2_PROFILE ] ; then
+        echo "WARNING: GN2_PROFILE has not been set - I hope you know what you are doing"
+    else
+        export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages
+        export R_LIBS_SITE=$GN2_PROFILE/site-library
+        export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
+        export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
+        export XDG_DATA_DIRS="$GN2_PROFILE/share"
+        export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules"
+    fi
+    if [ -z $PYTHONPATH ] ; then
+        echo "WARNING PYTHONPATH has not been set"
+    fi
+    if [ ! -d $R_LIBS_SITE ] ; then
+        echo "ERROR: R_LIBS_SITE has not been set correctly (we only allow one path)"
+        echo "Paste in the output of, for example,"
+        echo "guix package -p /usr/local/guix-profiles/gn2-staging --search-paths"
+        exit 1
+    fi
+fi
+
 # We may change this one:
-export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH
+export PYTHONPATH=$GN2_BASE_DIR/wqflask:$PYTHONPATH
 
 # TEMPDIR defaults to /tmp if nothing else
 if [ -z $TEMPDIR ]; then
     TEMPDIR="/tmp"
 fi
 
+set|grep $GN2_PROFILE
+set|grep TEMPDIR
+
 # Now handle command parameter -c
 if [ "$1" = '-c' ] ; then
-    cd $GN2_BASE_PATH/wqflask
+    cd $GN2_BASE_DIR/wqflask
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
     echo RUNNING COMMAND $cmd
@@ -71,6 +101,6 @@ dbfilename gn2.rdb
 " | redis-server - &
 
 # Start the flask server running GN2
-cd $GN2_BASE_PATH/wqflask
+cd $GN2_BASE_DIR/wqflask
 echo "Starting with $settings"
 /usr/bin/env python runserver.py
-- 
cgit v1.2.3


From 74ae90740b4d0b305199474359056fe4123224b1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 5 Oct 2016 06:52:34 +0000
Subject: Testing: show --all option

---
 bin/test-website | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'bin')

diff --git a/bin/test-website b/bin/test-website
index b693bd60..c9a72a5e 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -15,6 +15,10 @@ If you are using the small deployment database you can use
 
   ./bin/test-website --skip -n
 
+To run all tests
+
+  ./bin/test-website --all
+
 To run individual tests on localhost you can do
 
   ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
-- 
cgit v1.2.3